Notes on: Single-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells

| 13 Comments

Brief background:

We have two copies of each non-sex gene. Each version of the gene is called an allele: one inherited from your genetic mother, one from your genetic father. It is generally thought that each allele is expressed (turned out) at the same intensity. But, there are some examples where this isn’t true. The most notable occurs on the X chromosome. Females with two X chromosomes inherited one X chromosome from each parent, but one of these X chromosomes is almost completely inactivated. That means that instead of having biallelic expression (expression from both the maternal and paternal allele), most genes on the X chromosome exhibit monoallelic expression.

In recent work, Deng et al (2014) isolated single cells from two different stains of mice, where they could detect maternal-alleles and paternal-alleles for over 82% of assayed genes (in the other genes, there were not unique variants that allowed deciphering between the two alleles). For each gene, the authors characterized whether they could detect expression from both the maternal and paternal alleles, or from only the maternal or paternal allele. Although the title says, “mammalian,” all of the experiments and analysis were conducted in mouse cells and tissues, so far as I can tell.

My notes and thoughts on the paper:

  • The authors state, “…different SNPs within the same gene gave coherent allelic calls (fig. S2).” I am very interested to see what they did in cases where different SNPs did not give the same estimates of allele-specific expression.
  • Mouse paternal X chromosome inactivation is complicated. In single cells, the paternal X chromosome is inactive initially, reactivated starting at the late 2-cell stage, active at the 4-cell stage, then inactivated starting at the 16-cell stage, and completely inactivated again by the early blastocyst stage. Xist appears to be off during early embryogensis, and is only expressed starting at the 16-cell stage - correlating with the re-silencing of the paternal X chromosome in the mouse.
  • X-inactivation near and far from mouse XIC. The spread of X-inactivation is not directly correlated to the distance from the X-inactivation center (XIC).
  • Technology biases estimates of allele-specific expression. Initial observations of allele-specific expression on the autosomes suggested over half of all genes exhibit mono-allelic expression, but as much as 66% of these are false positives due to the loss of RNA molecules with the available technology. After inferring the proportion of losses RNA molecules, the authors propose that 12-24% of genes exhibit monoallelic expression in single cells.
  • Monoallelic expression evens out in tissues. The authors state, “Pooling cells by embryo removed essentially all monoallelic expression, demonstrating a high degree of cell-specific randomness in monoallelic expression.” To me this suggests that studies of single cell gene expression may not give the most accurate picture of gene expression within a tissue. 

Additional thoughts:

  • I would very much like to know how estimates of allele-specific expression on the X chromosome varied between the single cell and multicelluar analyses. 
  • The authors claim the patterns of monoallelic expression on the autosomes is likely due to independent allelic expression, but I would like to understand the mechanism more. Is this simply variance in polymerase activity? 
  • If 12-24% of genes are expressed from only one allele, what can we learn from it? Is dosage of these genes less important? Is selection weaker on genes that are more likely to be mono-allelicly expressed? 


Science. 2014 Jan 10;343(6167):193-6. doi: 10.1126/science.1245316.

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.

13 Comments

First line typo - “done inherited from your genetic mother” should be “one inherited from your genetic mother”.

I vaguely remember reading a suggestion that the paternally derived X is more likely to be inactivated than its homolog. Is this correct or a figment of my imagination?

Your post mentions X chromosomes a lot. The reader could get the impression that Deng et al. were studying only X-linked genes. But they were actually (at least judging by their paper’s abstract) studying mostly autosomal genes.

So their result is a surprise. There are two copies, but even in chromosomes that are not subject to X-inactivation, only one copy is functioning in most cells. It is randomly one or the other, so there seems to be no systematic suppression of activity of one copy. Even leaving aside what their study says about X-inactivation, their results are remarkable.

If only one copy is functioning in most cells, is it the copy from the parent that is functional for the X chromosome in females? Does the other copy get expressed at all, even at low levels? Does the expression pattern change over time or in response to any environmental factors? What is the functional significance of this finding, if any? How do creationists (except byers) explain this?

They ascribe their own results to transcriptional bursting, which is not (I gather) either new or particularly surprising. (This observation led to the comment by Michael Eisen, “So when I’m running and only one foot is on the ground I’m not bipedal”, and the response by Leonid Kruglyak, “‘Dynamic, random monopedal stance in human runners…’”)

Paul Burnett said:

First line typo - “done inherited from your genetic mother” should be “one inherited from your genetic mother”.

Nah, that’s just how we done learned to talk down here.

Paul Burnett said:

First line typo - “done inherited from your genetic mother” should be “one inherited from your genetic mother”.

Thank you :)

Here is the Storify of the discussion on twitter about this result, and how it is transcriptional bursting. I wasn’t aware of the term, so here’s the wikipedia entry for transcriptional bursting. Given this background, it is not so surprising that there is so much variation in expression across the autosomes, but my questions about what kind of classes exhibit measurable levels of this phenomenon in single cells still stands.

Also, I did focus on the X chromosome results because to me they were the most interesting. In marsupials it is always the paternal X that is inactivated - there is no random X-inactivation. My understanding is that in eutherian mammals the paternal X is inherited as inactivated, it is reactivated, then either the maternal or paternal allele is randomly inactivated. That said, there is some evidence of preferential paternal X-inactivation in mice - see Paternally biased X inactivation in mouse neonatal brain.

Hmmm. Do the activation/inactivation patterns generally remain constant over a cell’s lifetime? Could an allele from the maternal chromosome be active part of the time and then be shifted to the paternal copy at intervals throughout the cell’s life? Or could both allele’s be active part of the time and only one active for another part of the time?

This even implies the possibility that both genes might sometimes go silent…

https://me.yahoo.com/a/GQ2PdCNxj48x[…]r_p5YA#ff82e said:

Hmmm. Do the activation/inactivation patterns generally remain constant over a cell’s lifetime? Could an allele from the maternal chromosome be active part of the time and then be shifted to the paternal copy at intervals throughout the cell’s life? Or could both allele’s be active part of the time and only one active for another part of the time?

This even implies the possibility that both genes might sometimes go silent…

As far as I know, once a Barr body is formed (meaning one X chromosome has been mostly inactivated), it stays that way forever.

Now, this transcriptional bursting across the autosomes, appears to be a stochastic process, and so depending on when it is assayed, one may detect transcription from only the maternal allele, only the paternal allele, both, or neither (likely for lowly expressed genes).

Joe Felsenstein said: Even leaving aside what their study says about X-inactivation, their results are remarkable.

Steve Schaffner

They ascribe their own results to transcriptional bursting, which is not (I gather) either new or particularly surprising.

<blush> Shows how much I know about molecular biology. </blush>

Joe Felsenstein said:

Joe Felsenstein said: Even leaving aside what their study says about X-inactivation, their results are remarkable.

Steve Schaffner

They ascribe their own results to transcriptional bursting, which is not (I gather) either new or particularly surprising.

<blush> Shows how much I know about molecular biology. </blush>

Hey, all I know is what I read on twitter.

Twittering is for the birds.

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This page contains a single entry by M. Wilson Sayres published on January 26, 2014 9:36 PM.

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